/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
/**
* PredFile.java
* JalviewX / Vamsas Project
* JPred.seq.concise reader
- */\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class JPredFile extends AlignFile {\r
- Vector ids;\r
- Vector conf;\r
- Hashtable Scores; // Hash of names and score vectors\r
- Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector\r
- private int QuerySeqPosition;\r
-\r
- public JPredFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public JPredFile(String inFile, String type) throws IOException {\r
- super(inFile, type);\r
- }\r
-\r
- public void setQuerySeqPosition(int QuerySeqPosition) {\r
- this.QuerySeqPosition = QuerySeqPosition;\r
- }\r
-\r
- public int getQuerySeqPosition() {\r
- return QuerySeqPosition;\r
- }\r
-\r
- public Hashtable getScores() {\r
- return Scores;\r
- }\r
-\r
- public Hashtable getSymscores() {\r
- return Symscores;\r
- }\r
-\r
- public void initData() {\r
- super.initData();\r
- Scores = new Hashtable();\r
- ids = null;\r
- conf = null;\r
- }\r
-\r
- /**
- * parse a JPred concise file into a sequence-alignment like object.
- */\r
- public void parse() throws IOException {\r
- // JBPNote log.System.out.println("all read in ");\r
- String line;\r
- QuerySeqPosition = -1;\r
- noSeqs = 0;\r
-\r
- Vector seq_entries = new Vector();\r
- Vector ids = new Vector();\r
- Hashtable Symscores = new Hashtable();\r
-\r
- while ((line = nextLine()) != null) {\r
- // Concise format allows no comments or non comma-formatted data\r
- StringTokenizer str = new StringTokenizer(line, ":");\r
- String id = "";\r
-\r
- if (!str.hasMoreTokens()) {\r
- continue;\r
- }\r
-\r
- id = str.nextToken();\r
-\r
- String seqsym = str.nextToken();\r
- StringTokenizer symbols = new StringTokenizer(seqsym, ",");\r
-\r
- // decide if we have more than just alphanumeric symbols\r
- int numSymbols = symbols.countTokens();\r
-\r
- if (numSymbols == 0) {\r
- continue;\r
- }\r
-\r
- if (seqsym.length() != (2 * numSymbols)) {\r
- // Set of scalars for some property\r
- if (Scores.containsKey(id)) {\r
- int i = 1;\r
-\r
- while (Scores.containsKey(id + "_" + i)) {\r
- i++;\r
- }\r
-\r
- id = id + "_" + i;\r
- }\r
-\r
- Vector scores = new Vector();\r
-\r
- // Typecheck from first entry\r
- int i = 0;\r
- String ascore = "dead";\r
-\r
- try {\r
- // store elements as floats...\r
- while (symbols.hasMoreTokens()) {\r
- ascore = symbols.nextToken();\r
-\r
- Float score = new Float(ascore);\r
- scores.addElement((Object) score);\r
- }\r
-\r
- Scores.put(id, scores);\r
- } catch (Exception e) {\r
- // or just keep them as strings\r
- i = scores.size();\r
-\r
- for (int j = 0; j < i; j++) {\r
- scores.set(j,\r
- (Object) ((Float) scores.get(j)).toString());\r
- }\r
-\r
- scores.addElement((Object) ascore);\r
-\r
- while (symbols.hasMoreTokens()) {\r
- ascore = symbols.nextToken();\r
- scores.addElement((Object) ascore);\r
- }\r
-\r
- Scores.put(id, scores);\r
- }\r
- } else if (id.equals("jnetconf")) {\r
- // log.debug System.out.println("here");\r
- id = "Prediction Confidence";\r
- this.conf = new Vector(numSymbols);\r
-\r
- for (int i = 0; i < numSymbols; i++) {\r
- conf.set(i, (Object) symbols.nextToken());\r
- }\r
- } else {\r
- // Sequence or a prediction string (rendered as sequence)\r
- StringBuffer newseq = new StringBuffer();\r
-\r
- for (int i = 0; i < numSymbols; i++) {\r
- newseq.append(symbols.nextToken());\r
- }\r
-\r
- if (id.indexOf(";") > -1) {\r
- seq_entries.addElement(newseq);\r
-\r
- int i = 1;\r
- String name = id.substring(id.indexOf(";") + 1);\r
-\r
- while (ids.lastIndexOf(name) > -1) {\r
- name = id.substring(id.indexOf(";") + 1) + "_" + 1;\r
- }\r
-\r
- ids.addElement(name);\r
-\r
- noSeqs++;\r
- } else {\r
- if (id.equals("JNETPRED")) {\r
- id = "Predicted Secondary Structure";\r
- }\r
-\r
- seq_entries.addElement(newseq.toString());\r
- ids.addElement(id);\r
- Symscores.put((Object) id,\r
- (Object) new Integer(ids.size() - 1));\r
- }\r
- }\r
- }\r
-\r
- if (noSeqs < 1) {\r
- throw new IOException(\r
- "JpredFile Parser: No sequence in the prediction!");\r
- }\r
-\r
- maxLength = seq_entries.elementAt(0).toString().length();\r
-\r
- for (int i = 0; i < ids.size(); i++) {\r
- // Add all sequence like objects\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seq_entries.elementAt(i).toString(), 1,\r
- seq_entries.elementAt(i).toString().length());\r
-\r
- if (!Symscores.containsKey(ids.elementAt(i)) &&\r
- !isValidProteinSequence(newSeq.getSequence())) {\r
- throw new IOException(\r
- "JPredConcise: Not a valid protein sequence - (" +\r
- ids.elementAt(i).toString() + ")");\r
- }\r
-\r
- if (maxLength != seq_entries.elementAt(i).toString().length()) {\r
- throw new IOException("JPredConcise: Entry (" +\r
- ids.elementAt(i).toString() +\r
- ") has an unexpected number of columns");\r
- }\r
-\r
- if (newSeq.getName().startsWith("QUERY") &&\r
- (QuerySeqPosition == -1)) {\r
- QuerySeqPosition = seqs.size();\r
- }\r
-\r
- seqs.addElement(newSeq);\r
- }\r
- }\r
-\r
- /**
- * print
- *
- * @return String
- */\r
- public String print() {\r
- return "Not Supported";\r
- }\r
-\r
- public static void main(String[] args) {\r
- try {\r
- JPredFile blc = new JPredFile(args[0], "File");\r
-\r
- for (int i = 0; i < blc.seqs.size(); i++) {\r
- System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() +\r
- "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequence() +\r
- "\n");\r
- }\r
- } catch (java.io.IOException e) {\r
- System.err.println("Exception " + e);\r
- e.printStackTrace();\r
- }\r
- }\r
-}\r
-\r
-\r
-/*
- StringBuffer out = new StringBuffer();
-
- out.append("START PRED\n");
- for (int i = 0; i < s[0].sequence.length(); i++)
- {
- out.append(s[0].sequence.substring(i, i + 1) + " ");
- out.append(s[1].sequence.substring(i, i + 1) + " ");
- out.append(s[1].score[0].elementAt(i) + " ");
- out.append(s[1].score[1].elementAt(i) + " ");
- out.append(s[1].score[2].elementAt(i) + " ");
- out.append(s[1].score[3].elementAt(i) + " ");
-
- out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
- public static void main(String[] args)
- {
- try
+ */
+package jalview.io;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+/**
+ * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
+ * line is either a sequence (QUERY), a sequence profile (align;), or jnet
+ * prediction annotation (anything else). Automagic translation happens for
+ * annotation called 'JNETPRED' (translated to Secondary Structure Prediction),
+ * or 'JNETCONF' (translates to 'Prediction Confidence'). Numeric scores are
+ * differentiated from symbolic by being parseable into a float vector. They are
+ * put in Scores. Symscores gets the others. JNetAnnotationMaker translates the
+ * data parsed by this object into annotation on an alignment. It is
+ * automatically called but can be used to transfer the annotation onto a
+ * sequence in another alignment (and insert gaps where necessary)
+ *
+ * @author jprocter
+ * @version $Revision$
+ */
+public class JPredFile extends AlignFile
+{
+ Vector ids;
+
+ Vector conf;
+
+ Hashtable Scores; // Hash of names and score vectors
+
+ Hashtable Symscores; // indexes of symbol annotation properties in sequenceI
+
+ // vector
+
+ private int QuerySeqPosition;
+
+ /**
+ * Creates a new JPredFile object.
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public JPredFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public JPredFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param QuerySeqPosition
+ * DOCUMENT ME!
+ */
+ public void setQuerySeqPosition(int QuerySeqPosition)
+ {
+ this.QuerySeqPosition = QuerySeqPosition;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getQuerySeqPosition()
+ {
+ return QuerySeqPosition;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getScores()
+ {
+ return Scores;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getSymscores()
{
- BLCFile blc = new BLCFile(args[0], "File");
- DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
- for (int i = 0; i < blc.seqs.size(); i++)
+ return Symscores;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initData()
+ {
+ super.initData();
+ Scores = new Hashtable();
+ ids = null;
+ conf = null;
+ }
+
+ /**
+ * parse a JPred concise file into a sequence-alignment like object.
+ */
+ public void parse() throws IOException
+ {
+ // JBPNote log.System.out.println("all read in ");
+ String line;
+ QuerySeqPosition = -1;
+ noSeqs = 0;
+
+ Vector seq_entries = new Vector();
+ Vector ids = new Vector();
+ Hashtable Symscores = new Hashtable();
+
+ while ((line = nextLine()) != null)
+ {
+ // Concise format allows no comments or non comma-formatted data
+ StringTokenizer str = new StringTokenizer(line, ":");
+ String id = "";
+
+ if (!str.hasMoreTokens())
+ {
+ continue;
+ }
+
+ id = str.nextToken();
+
+ String seqsym = str.nextToken();
+ StringTokenizer symbols = new StringTokenizer(seqsym, ",");
+
+ // decide if we have more than just alphanumeric symbols
+ int numSymbols = symbols.countTokens();
+
+ if (numSymbols == 0)
+ {
+ continue;
+ }
+
+ if (seqsym.length() != (2 * numSymbols))
+ {
+ // Set of scalars for some property
+ if (Scores.containsKey(id))
+ {
+ int i = 1;
+
+ while (Scores.containsKey(id + "_" + i))
+ {
+ i++;
+ }
+
+ id = id + "_" + i;
+ }
+
+ Vector scores = new Vector();
+
+ // Typecheck from first entry
+ int i = 0;
+ String ascore = "dead";
+
+ try
+ {
+ // store elements as floats...
+ while (symbols.hasMoreTokens())
+ {
+ ascore = symbols.nextToken();
+
+ Float score = new Float(ascore);
+ scores.addElement((Object) score);
+ }
+
+ Scores.put(id, scores);
+ } catch (Exception e)
+ {
+ // or just keep them as strings
+ i = scores.size();
+
+ for (int j = 0; j < i; j++)
+ {
+ scores.setElementAt(
+ (Object) ((Float) scores.elementAt(j)).toString(), j);
+ }
+
+ scores.addElement((Object) ascore);
+
+ while (symbols.hasMoreTokens())
+ {
+ ascore = symbols.nextToken();
+ scores.addElement((Object) ascore);
+ }
+
+ Scores.put(id, scores);
+ }
+ }
+ else if (id.equals("jnetconf"))
+ {
+ // log.debug System.out.println("here");
+ id = "Prediction Confidence";
+ this.conf = new Vector(numSymbols);
+
+ for (int i = 0; i < numSymbols; i++)
+ {
+ conf.setElementAt(symbols.nextToken(), i);
+ }
+ }
+ else
+ {
+ // Sequence or a prediction string (rendered as sequence)
+ StringBuffer newseq = new StringBuffer();
+
+ for (int i = 0; i < numSymbols; i++)
+ {
+ newseq.append(symbols.nextToken());
+ }
+
+ if (id.indexOf(";") > -1)
+ {
+ seq_entries.addElement(newseq);
+
+ int i = 1;
+ String name = id.substring(id.indexOf(";") + 1);
+
+ while (ids.lastIndexOf(name) > -1)
+ {
+ name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
+ }
+
+ if (QuerySeqPosition == -1)
+ QuerySeqPosition = ids.size();
+ ids.addElement(name);
+ noSeqs++;
+ }
+ else
+ {
+ if (id.equals("JNETPRED"))
+ {
+ id = "Predicted Secondary Structure";
+ }
+
+ seq_entries.addElement(newseq.toString());
+ ids.addElement(id);
+ Symscores.put((Object) id, (Object) new Integer(ids.size() - 1));
+ }
+ }
+ }
+ /*
+ * leave it to the parser user to actually check this. if (noSeqs < 1) {
+ * throw new IOException( "JpredFile Parser: No sequence in the
+ * prediction!"); }
+ */
+
+ maxLength = seq_entries.elementAt(0).toString().length();
+
+ for (int i = 0; i < ids.size(); i++)
+ {
+ // Add all sequence like objects
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
+ seq_entries.elementAt(i).toString(), 1, seq_entries
+ .elementAt(i).toString().length());
+
+ if (maxLength != seq_entries.elementAt(i).toString().length())
+ {
+ throw new IOException(
+ MessageManager
+ .formatMessage(
+ "exception.jpredconcide_entry_has_unexpected_number_of_columns",
+ new String[] { ids.elementAt(i).toString() }));
+ }
+
+ if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
+ .startsWith("align;")) && (QuerySeqPosition == -1))
+ {
+ QuerySeqPosition = seqs.size();
+ }
+
+ seqs.addElement(newSeq);
+ }
+ if (seqs.size() > 0 && QuerySeqPosition > -1)
{
- s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
+ // try to make annotation for a prediction only input (default if no
+ // alignment is given and prediction contains a QUERY or align;sequence_id
+ // line)
+ Alignment tal = new Alignment(this.getSeqsAsArray());
+ try
+ {
+ JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition,
+ true);
+ } catch (Exception e)
+ {
+ tal = null;
+ IOException ex = new IOException(
+ MessageManager
+ .formatMessage(
+ "exception.couldnt_parse_concise_annotation_for_prediction",
+ new String[] { e.getMessage() }));
+ e.printStackTrace(); // java 1.1 does not have :
+ // ex.setStackTrace(e.getStackTrace());
+ throw ex;
+ }
+ this.annotations = new Vector();
+ AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
+ for (int aai = 0; aan != null && aai < aan.length; aai++)
+ {
+ annotations.addElement(aan[aai]);
+ }
}
- String out = BLCFile.print(s);
+ }
- AlignFrame af = new AlignFrame(null, s);
- af.resize(700, 500);
- af.show();
- System.out.println(out);
+ /**
+ * print
+ *
+ * @return String
+ */
+ public String print()
+ {
+ return "Not Supported";
}
- catch (java.io.IOException e)
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args)
+ {
+ try
+ {
+ JPredFile blc = new JPredFile(args[0], "File");
+
+ for (int i = 0; i < blc.seqs.size(); i++)
+ {
+ System.out.println(((Sequence) blc.seqs.elementAt(i)).getName()
+ + "\n"
+ + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString()
+ + "\n");
+ }
+ } catch (java.io.IOException e)
+ {
+ System.err.println("Exception " + e);
+ // e.printStackTrace(); not java 1.1 compatible!
+ }
+ }
+
+ Vector annotSeqs = null;
+
+ /**
+ * removeNonSequences
+ */
+ public void removeNonSequences()
{
- System.out.println("Exception " + e);
+ if (annotSeqs != null)
+ {
+ return;
+ }
+ annotSeqs = new Vector();
+ Vector newseqs = new Vector();
+ int i = 0;
+ int j = seqs.size();
+ for (; i < QuerySeqPosition; i++)
+ {
+ annotSeqs.addElement(seqs.elementAt(i));
+ }
+ // check that no stray annotations have been added at the end.
+ {
+ SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
+ if (sq.getName().toUpperCase().startsWith("JPRED"))
+ {
+ annotSeqs.addElement(sq);
+ seqs.removeElementAt(--j);
+ }
+ }
+ for (; i < j; i++)
+ {
+ newseqs.addElement(seqs.elementAt(i));
+ }
+
+ seqs.removeAllElements();
+ seqs = newseqs;
}
- }
+}
- }
- */\r
+/*
+ * StringBuffer out = new StringBuffer();
+ *
+ * out.append("START PRED\n"); for (int i = 0; i < s[0].sequence.length(); i++)
+ * { out.append(s[0].sequence.substring(i, i + 1) + " ");
+ * out.append(s[1].sequence.substring(i, i + 1) + " ");
+ * out.append(s[1].score[0].elementAt(i) + " ");
+ * out.append(s[1].score[1].elementAt(i) + " ");
+ * out.append(s[1].score[2].elementAt(i) + " ");
+ * out.append(s[1].score[3].elementAt(i) + " ");
+ *
+ * out.append("\n"); } out.append("END PRED\n"); return out.toString(); }
+ *
+ * public static void main(String[] args) { try { BLCFile blc = new
+ * BLCFile(args[0], "File"); DrawableSequence[] s = new
+ * DrawableSequence[blc.seqs.size()]; for (int i = 0; i < blc.seqs.size(); i++)
+ * { s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); } String
+ * out = BLCFile.print(s);
+ *
+ * AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
+ * System.out.println(out); } catch (java.io.IOException e) {
+ * System.out.println("Exception " + e); } } }
+ */
git://source.jalview.org / jalview.git / blobdiff